Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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De novo comparative transcriptome analyses of strawberry (Fragaria vesca) genotypes in response to Phytophthora cactorum.

ABSTRACT: In this RNA-seq study, we compared the transcriptome of three Fragaria vesca genotypes in response to Phytophthora cactorum. The goal of our study was to dissect the resistance mechanism of the diploid strawberry (F. vesca) that are resistant to P. cactorum. A susceptible genotype (NCGR1218) and two resistant (NCGR1603 and Bukammen) F. vesca genotypes were used for the comparative transcriptome analyses. Plants were inoculated with P. cactorum zoospores (2mL of 2 × 105 spores/mL) in the crown (rhizome) and sampled 48 hours later. The appropriate controls for each genotype were i) samples wounded and inoculated with water and sampled 48 hours after the treatment and ii) untreated samples. Four biological replicates, each consisting of four individual test plants from each genotype were used for the transcriptome study. All the samples were collected from the crown, flash-frozen in liquid nitrogen and stored at -80 °C until RNA isolation. Total RNA was isolated using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer’s instructions. For sequencing, the libraries were prepared using the TruSeqTM stranded total RNA library prep kit (Illumina, USA), indexed and pooled, and sequenced in four lanes using the Illumina HiSeq 3/4000 (2×150 bp) System by the Norwegian Sequencing Centre, Oslo, Norway. Raw reads were quality filtered, de novo assembled into transcripts and were analysed for differentially expressed genes between the inoculated and control samples.

INSTRUMENT(S): Illumina HiSeq 3000

ORGANISM(S): Fragaria vesca

SUBMITTER: Anupam Gogoi

PROVIDER: E-MTAB-12152 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease.The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/Phytophthora parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy.The present project aims at analyzing the compatible interaction between A. thaliana roots and Phytophthora parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom designed Phytophthora parasitica biochip will enable analyzing of Phytophthora parasitica gene expression during the same stages. The pathosystem involving A. thaliana and Phytophthora parasitica was described in Attard A, Gourgues M, Callemeyn-Torre N, Keller H. 2010. The New phytologist 187: 449–460. The protocol for recovery of RNA from purified appressoria was described in Kebdani N, Pieuchot L, Deleury E, Panabieres F, Le Berre JY, Gourgues M. 2010. New Phytol 185: 248–257. A series of 14 hybridizations corresponding to two biological replicates each corresponding to RNA extractions of the following biological conditions were used: 1-Vegetative mycelium (recovered from two samples of 4 day-old cultures in liquid V8 medium at 24°C), 2- Motile zoospores (recovered from 8 independent cultures), 3-Appressoria differentiated on onion epidermis (epidermis from 20 onion bulbs inoculated with zoospores collected from 8 independent Petri dishes); appressoria collected 3 hours after inoculation (24 °C), 5- Infection of A. thaliana roots by Phytophthora parasitica zoospores (samples recovered at 2.5, 6, 10.5 and 30 hours post inoculation; 5 inoculated plants for each sample).

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De novo comparative transcriptome analyses of strawberry (Fragaria vesca) genotypes in response to Phytophthora cactorum.

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